Freesurfer March 2024

freesurfer@nmr.mgh.harvard.edu

58 participants
61 discussions

aparc & wm underestimation
by Stanica, Maria 29 Mar '24

29 Mar '24

External Email - Use Caution Hello FS developers, I ran my subjects through skullstripping and recon-all. Everything processed correctly (and exited without errors), except 4 images which have an underestimation in coronal subcortical region. The underestimation is significant and goes on for about 10-12 slices (for one image it was 153-162, for another it was 150-164). After searching the list, we attempted control points, which ended up not working (I don’t believe this was the right method to correct the error). Then we tried white matter edits, and one of the images was resolved, but the other 3 did not get better. Is there anything else we could do to try to resolve the issue? I can provide any other information needed. Any help would be appreciated! 1. Freesurfer version: FreeSurfer/7.1.1-centos7_x86_64 2. Operating System: Red Hat Enterprise Linux 7 3. OS Version: 7.9 (Maipo) Best, Maria Maria Stǎnicǎ, B.A. | Graduate Student Medical/Clinical Psychology Doctoral Program UAB |The University of Alabama at Birmingham mstanica(a)uab.edu<mailto:mstanica@uab.edu> Pronouns: she/her/hers [Image]

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recon-all nu_correct error
by Dong, Yilei 28 Mar '24

28 Mar '24

External Email - Use Caution Hi Freesurfer support, Recently, I submitted a script to run recon-all on 100 MRI images on UCSD's computing cluster. I get an error file that says "nu_correct: Command not found. FREESURFER: Undefined variable." I previously emailed this problem and was told to send my recon-all.log if running the recon-all did not work a 2nd time. I was also told previously that my cluster's Freesurfer can't locate the minc toolkit binaries on my system. How can this error be troubleshooted? Please let me know if you need any other information. Freesurfer version: 7.2.0, but already available as module Platform: Rocky Linux release 8.8 (Green Obsidian) uname -a: Linux login01 4.18.0-477.15.1.el8_8.x86_64 #1 SMP Wed Jun 28 15:04:18 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux Recon-all log: see attached Sincerely, Yilei

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command line options to control appearance in timecourse window
by Proulx, Jean Sebastien 27 Mar '24

27 Mar '24

Dear Fresurfers, I'm visualizing multiple timecourses using the -timecourse window in freeview. I'd like to specify the color of each traces through the command line. Is there a hidden (or easy to implement) feature for that? I use the dev version at the Martinos. Thanks for the help and Have a great day! Sebastien

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Unexpected cortical expansion in the anterior cingulate
by Gordon, Brian 25 Mar '24

25 Mar '24

External Email - Use Caution I saw this paper making the rounds recently (https://secure-web.cisco.com/1xpFxsKoB351lR8nLgcY1jLc9MKM9SFg22L-Gj-yGOtM9a…) arguing that there are some areas where the cortex appears thicker with advancing Alzheimer Disease. The paper points towards prior publications from my own group which studies autosomal dominant AD where similar effects were found albeit did not reach significance. I've also seen this unexpected directional reversal in other cohorts. For aging I've seen it as far back as 2004 (https://secure-web.cisco.com/1exfvo1PFoqzlNRA3kd-j6t_3mH_q9fK-YbuHkw-gMEwFD…) Have others seen this? I don't tend to think of their being true increases in thickness in neurodegenerative diseases, although I guess it could have occurred. I've always wondered if instead it had to do with some sort of bias or quirk that is coming into play when you have large displacement of this region due to expanding ventricles. I was just curious if other groups had seen this and if so with what disorders. ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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nu_correct: Command not found error
by Dong, Yilei 25 Mar '24

25 Mar '24

External Email - Use Caution Hi Freesurfer support, Recently, I submitted a script to run recon-all on 100 mri images on UCSD's computing cluster, called EXPANSE. I get an error file that says "nu_correct: Command not found. FREESURFER: Undefined variable." The sample error file and the output file I have attached for one of the subjects are recon-all-slurm.29376886.exp-5-44.err & recon-all-slurm.29376886.exp-5-44.out respectively. The script I used to submit the job via slurm is called recon-all-slurm.sb. I googled the error and found that someone else who had a similar situation did not source their Freesurfer environment correctly. Would this be the same thing for us as well? The main thing for us is Freesurfer/7.2.0 already has been available as a module for us on EXPANSE. Sincerely, Yilei

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Lab Manager Position in Cognitive Neuroscience at Tulane University
by Ben Deen 25 Mar '24

25 Mar '24

External Email - Use Caution The Social Memory Lab at Tulane University, directed by Dr. Benjamin Deen, is seeking a Laboratory Research Technician who will contribute to multiple aspects of projects studying social perception, cognition, and memory, using behavioral and neuroimaging (fMRI) methods. The Laboratory Research Technician will work as part of a team comprised of postdoctoral fellows, graduate students, and undergraduate research assistants, and will coordinate day-to-day operations of the lab. Major responsibilities include participant recruitment, collection of behavioral and fMRI data, data analysis using Matlab or Python, and administrative duties. Other tasks will be commensurate with the experience and interests of the technician. The position requires excellent communication and organizational skills, a high degree of independence, and an interest in cognitive neuroscience. REQUIRED EDUCATION AND EXPERIENCE: 1. Bachelor’s degree in psychology, neuroscience, computer science, or a related field 2. Previous experience working in a research lab REQUIRED KNOWLEDGE, SKILLS, ABILITIES/COMPETENCIES 1. Ability to communicate effectively with lab members, university staff, and volunteers 2. Ability to perform daily tasks in a highly organized fashion, with attention to detail 3. Strong time management skills and ability to effectively manage multiple assignments 4. Willingness to work flexible hours, including evenings and weekends as needed 5. Desire to acquire new skills and competencies in a dynamic research atmosphere 6. Proficiency in computer skills, including Microsoft Office applications PREFERRED QUALIFICATIONS: 1. Proficiency coding in Matlab, Python, or R 2. Demonstrated interest in cognitive neuroscience research Interested candidates may find more information at https:// https://secure-web.cisco.com/1dgIq0ZuY6vnd7BNvgEMRYn0sJGQr-tkwT-mYIebzw5YxM…, apply online at https://secure-web.cisco.com/1kHinyl1Dz2ABzJrO2sX9PBs00gFIaWSiZcGKK3O1gt7am… or email bdeen(a)tulane.edu with any questions about the position.

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recon-all mris_preproc error: Cannot find surf/lh.w-g.pct.mgh
by Dan Levitas 25 Mar '24

25 Mar '24

External Email - Use Caution Hello, I have a longitudinal dataset where each participant was scanned twice over the course of 5 months. I have been following FS's Longitudinal Tutorial <https://secure-web.cisco.com/1cEj8JFOeCVl553obrTrsTW9AP-8Qv0LHSe3IerGFGTmaP…> . For the CROSS section, each subjects' session scan successfully completed recon-all, where I used the following command: *recon-all \* * -subjid sub-${sub}_ses-${ses} \ -i $raw_anat_file \ -qcache \ -all* I then used the following recon-all command for the BASE section: *recon-all \ -base sub-${sub}_year-1 \ -tp $subjects_dir/$pre_sub_ses \ -tp $subjects_dir/$post_sub_ses \ -qcache \ -all* This recon-all ran for several hours before failing at the following command: *mris_preproc --s sub-5009_year-1 --hemi lh --meas w-g.pct.mgh --target fsaverage --out lh.w-g.pct.mgh.fsaverage.mgh* The error message is: *nsubjects = 1ERROR: cannot find /N/project/Kawata_TBI_1/R01_HighSchool_BIDS/derivatives/freesurfer/sub-5009_year-1/surf/lh.w-g.pct.mghCommand exited with non-zero status 1@#@FSTIME 2024:03:21:02:30:48 mris_preproc N 10 e 0.09 S 0.05 U 0.02 P 82% M 3568 F 0 R 2201 W 0 c 2 w 45 I 0 O 0 L 60.94 63.09 63.23@#@FSLOADPOST 2024:03:21:02:30:48 mris_preproc N 10 60.94 63.09 63.23Linux c50.quartz.uits.iu.edu <http://secure-web.cisco.com/14Wbu8Wr5_K8JfIcqRcS1Cn5n2xX-aAI3fOWvKkmOStUpOW…> 4.18.0-513.9.1.el8_9.x86_64 #1 SMP Thu Nov 16 10:29:04 EST 2023 x86_64 x86_64 x86_64 GNU/Linux* *recon-all -s sub-5009_year-1 exited with ERRORS at Thu Mar 21 02:30:48 EDT 2024* I have checked the archive but can't seem to find a similar question. I'm a bit new to FreeSurfer, so I am unsure how to resolve this issue. I've attached the recon-all.log if that might help. *FreeSurfer version*: freesurfer-linux-centos8_x86_64-7.4.1-20230613-7eb8460 *Platform*: Red Hat Enterprise Linux 8.9 Ootpa) *uname -a*: Linux i48.red.uits.iu.edu 4.18.0-513.9.1.el8_9.x86_64 #1 SMP Thu Nov 16 10:29:04 EST 2023 x86_64 x86_64 x86_64 GNU/Linux *recon-all log*: see attached Thank you. Dan

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Using orig.mgz or T1.mgz as input to recon-all
by Jeong Yeon Kang 25 Mar '24

25 Mar '24

External Email - Use Caution Hello FreeSurfer Developers, I am attempting to run recon-all on a group of subjects. We no longer have the raw T1s. Instead, we have their orig.mgz and T1.mgz files from a previous run of freesurfer. We wish to rerun recon-all using their orig.mgz or T1.mgz as inputs, using FreeSurfer5.3. What would be the best way to go about this? 1. I ran recon-all normally, with orig.mgz as the input file. It ran to completion, but some files are missing from subdirectories. I am not sure if the outputs are correct, and comparable to other datasets that have freesurfer outputs that used raw T1s. 2. I converted orig.mgz to orig.nii.gz using mri_convert, and used orig.nii.gz as input to recon-all. This also ran to completion. However, because I cannot compare this output to any "true" output, I am unsure if the outputs are correct, and is the same as using a raw T1 as input. 3. I considered manually starting the recon process from T1.mgz (organizing subdirectories manually, inserting T1.mgz and orig.mgz into /mri, and starting autorecon2. I am unsure if this is best, as I am missing nu.mgz, which is an input file in the first step of autorecon2. Please let me know what you think, and which method you think would be closest to using the raw T1s. I've searched the list and it seems that no one has attempted a similar task. Thank you. Sincerely, Melody

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FW: Call for Program Coordinators (due March 27) -- SPARK Academy in Deep Learning and Medical Imaging
by Fischl, Bruce R.,PHD 24 Mar '24

24 Mar '24

See below for a great opportunity for grad students and postdocs Cheers Bruce From: Yao, Jingting,PHD, MS <JYAO0(a)mgh.harvard.edu> Sent: Saturday, March 23, 2024 10:36 PM To: Fischl, Bruce R.,PHD <BFISCHL(a)mgh.harvard.edu> Cc: Vanderkouwe, Andre,PHD <AVANDERKOUWE(a)mgh.harvard.edu>; donzhang(a)ece.ubc.ca; Udunna Anazodo, Dr <udunna.anazodo(a)mcgill.ca>; craymon8(a)uwo.ca Subject: Call for Program Coordinators (due March 27) -- SPARK Academy in Deep Learning and Medical Imaging Dear Bruce, Could you please share the fantastic opportunity detailed below with experienced machine learning PhD students and Postdoc fellows within your network? This initiative offers them the chance to contribute to the training of colleagues in Africa and Asia, providing a valuable opportunity for collaboration and knowledge exchange. Thank you for your assistance! Best, Jingting --- Jingting "Becky" Yao (she/her/hers) Postdoctoral Research Fellow Martinos Center for Biomedical Imaging Department of Radiology Massachusetts General Hospital/Harvard Medical School [cid:5125704d-814a-4278-8a31-6df04f19bd45] Call for Volunteers Dear colleagues, The Sprint AI Training for African Medical Imaging Knowledge Translation (SPARK)<https://c0ycp.r.sp1-brevo.net/mk/cl/f/Jd37qz89jOHnq_3HUB5tkoTCcab5O67lIhiXI…> Academy is designed to train a new generation of African artificial intelligence (AI) experts in medical imaging who can train others. In 2023, we ran the first SPARK Academy in collaboration with McMedHacks<https://c0ycp.r.sp1-brevo.net/mk/cl/f/_sPZfOBluW5UhuGFLmP9DwXX91Wks-rg1CePL…> and endorsed by the Medical Image Computing and Computer-Assisted Interventions (MICCAI) Society<https://c0ycp.r.sp1-brevo.net/mk/cl/f/l2aIxjJqtGGGQniT_trZMZ0mSo4uYqK6azvi0…>. We trained 70 researchers and clinicians from 15 countries, including 3 South East Asian countries. This first cohort developed 10 brain tumor segmentation models, 8 of which were ranked in the 2023 MICCAI brain tumor segmentation challenge competition, and 1 method was ranked in the top 2<https://c0ycp.r.sp1-brevo.net/mk/cl/f/Xa5kNSP96QF8MjKIQ-3cus2O4abCb8XAuRFT8…>. For 2024 we have received more than thrice the number of applications from Africa and South Asia. The 2024 cohort will work together to produce state-of-the-art AI methods for the 2024 MICCAI BraTS<https://c0ycp.r.sp1-brevo.net/mk/cl/f/4eZTrQjPRVT2KYD849Rr9SfMzS1oiCNF4CyKS…> Challenge, with top-ranked methods eligible for prizes. The purpose of this call is to invite passionate graduate students (MSc & PhD) and post-doctoral fellows with expertise in deep learning and medical imaging to join our team as volunteer Program Coordinators. This opportunity will provide graduate students with experiential peer-to-peer learning and leadership experience and help us prepare African teams to participate in grand challenges. With a time commitment of 4-6 hours per week, as a Program Coordinator you will be assigned to one team and will be required to: * Supervise a team to mentor them with their BraTS model development. * Facilitate in-person Hackathons under the direction of the Program Chairs. * Assist instructors during tutorial sessions, hackathons, and workshops. * Provide additional support and guidance to participants, especially during hands-on activities. * Help address technical questions and troubleshoot issues encountered by the team. * Grade assignments (no more than 4 assignments and once during the entire Academy). * Work with the team to draft their MICCAI conference paper, journal manuscripts, or presentations and serve as the senior author on conference papers and joint-senior author on journal papers. Call Deadline: March 27th 2024. Are you passionate about AI and medical imaging? Here's your chance to make a difference! Volunteer as a Program Coordinator for the 2024 SPARK Academy. Mentor, lead, and inspire Africa's future AI leaders. Volunteer applications should be submitted by March 27th as a 1-2-page CV with their name, affiliation, email address, career stage (PhD student or Postdoc), deep learning experience (programming language knowledge/skills and previous or ongoing projects). Please send your CV to Confidence Raymond (craymon8(a)uwo.ca<mailto:craymon8@uwo.ca>) and copy Dong Zhang (donzhang(a)ece.ubc.ca<mailto:donzhang@ece.ubc.ca>) with the email subject titled "SPARK Academy Program Coordinator Application". There is a 30-min Onboarding on March 29th. Event Page for More Details: https://event.fourwaves.com/spark<https://c0ycp.r.sp1-brevo.net/mk/cl/f/36kz1LxIUUyr0PFOQozLEm0wKhG6wo1zClkgJ…> Read about the 2023 SPARK Academy, here<https://c0ycp.r.sp1-brevo.net/mk/cl/f/ckZjWzY2M1PkWTj0D5TjWWxVQxbfswsiYI2KV…>. We look forward to receiving your applications! Please share this opportunity with your colleagues. Best regards, SPARK Academy (spark(a)mailab.io<mailto:spark@mailab.io>) The Consortium for Advancement of MRI Research and Education in Africa (CAMERA) [https://img-cache.net/im/6921921/5552a635561d4d09365e834d1b5ca6a83228eb2e31…]<https://c0ycp.r.sp1-brevo.net/mk/cl/f/u5dmxQAM1WXhB5CSuNMjnVwiqrYIeAqa77A7W…> [https://img-cache.net/im/6921921/2f08e48bc958e4c30dcf8be98435288cf9a83547ce…]<https://c0ycp.r.sp1-brevo.net/mk/cl/f/_5toX02YXqCotAe298Uq0QqMtAF9ElZWoThjc…> [https://img-cache.net/im/6921921/222244d31eb97bf87c97e39cfae167967c2db928fe…]<https://c0ycp.r.sp1-brevo.net/mk/cl/f/2fSM4GBC00347Z6Z_ZUMoTJP1c25Z6vSw8s4c…> [https://img-cache.net/im/6921921/123553018d4c988c79dd5349d671e48d4b9415b87d…]<https://c0ycp.r.sp1-brevo.net/mk/cl/f/hk3aw2q8ZngDJie2Xsd2AgpPlUy1St1nJizqE…>

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Re: [Freesurfer] if: Expression Syntax - preproc-sess
by Douglas N. Greve 22 Mar '24

22 Mar '24

Hi Stefano, I think I found and fixed the problem. Can you try these? On 3/19/2024 7:30 AM, Stefano Delli Pizzi wrote: > > External Email - Use Caution > > Hi Doug, > > The raw functional file is firstly passed with motion correction > (i.e., mc-sess -s ID -fsd rest -per-run) and AROMA filtering. > Next, I have renamed the ICA filtered file as f.nii.gz. > Then, I run: > > preproc-sess -s ${1} -surface fsaverage lhrh -nomc -fwhm 0 -mni305 > -fsd rest -per-run -sliceorder even -force > > There are issues with labels since excluding motion correction doesn't > produce key files necessary for concatenating the files. > The preprocessing script is searching for the fmcpr.nii.gz file, which > cannot be found because it is not created using the -nomc option. > > When I duplicate and rename the file f.nii.gz as fmcpr.nii.gz and > rerun preproc, the operation is done and the > fmcpr.odd.sm0.fsaverage.lh is created. > > However, when I run the next steps (fcseed-sess -s ID -cfg wm.config > -overwrite), a second error occurs (reported below) because the script > searches for fmcpr, which cannot be produced since I used -mc. > > ERROR: could not determine file for > /Volumes/mnu/MRI/PPMI/NIFTI/FreeSurfer/rs-fMRI_AROMA/ID/rest/001/fmcpr > This error seems to be related to the script searching for the fmcpr > file, which isn't available due to the use of -mc. > > Thank you. > > Best regards, > > > Stefano > > > > >> Il giorno 18 mar 2024, alle ore 17:16, Stefano Delli Pizzi >> <sdellipizzi(a)gmail.com> ha scritto: >> >> Hi Doug have you any news >> Thank you very much! >> Stefano >> >>> Il giorno 12 mar 2024, alle ore 10:26, Stefano Delli Pizzi >>> <sdellipizzi(a)gmail.com> ha scritto: >>> >>> Thank you. >>> I’m attaching the file. >>> Stefano >>> <preproc-sess> >>> >>>> Il giorno 11 mar 2024, alle ore 22:20, Douglas N. Greve >>>> <dgreve(a)mgh.harvard.edu> ha scritto: >>>> >>>> can you send me this file >>>> /Applications/freesurfer/7.4.1/fsfast/bin/preproc-sess >>>> >>>> >>>> On 3/11/2024 3:58 AM, Stefano Delli Pizzi wrote: >>>>> >>>>> External Email - Use Caution >>>>> >>>>> It seems to me that I've done what you suggest. Attached is a new >>>>> outputs. >>>>> Thanks >>>>> Stefano >>>>> >>>>>> Il giorno 10 mar 2024, alle ore 23:44, Douglas N. Greve >>>>>> <dgreve(a)mgh.harvard.edu> ha scritto: >>>>>> >>>>>> Are you sure that you are using the new version that I gave you? >>>>>> It looks like the previous version. Also, it does not look like >>>>>> the entire terminal output. >>>>>> >>>>>> On 3/8/2024 12:11 PM, Stefano Delli Pizzi wrote: >>>>>>> >>>>>>> External Email - Use Caution >>>>>>> >>>>>>> The entire terminal output is attached. >>>>>>> Thanks! >>>>>>> >>>>>>>> Il giorno 8 mar 2024, alle ore 15:56, Douglas N. Greve >>>>>>>> <dgreve(a)mgh.harvard.edu> ha scritto: >>>>>>>> >>>>>>>> entire terminal output >>>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> Freesurfer mailing list >>>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>> The information in this e-mail is intended only for the person to >>>>>> whom it is addressed. If you believe this e-mail was sent to you >>>>>> in error and the e-mail contains patient information, please >>>>>> contact the Mass General Brigham Compliance HelpLine at >>>>>> https://www.massgeneralbrigham.org/complianceline >>>>>> <https://www.massgeneralbrigham.org/complianceline> . >>>>> >>>> >>>> The information in this e-mail is intended only for the person to >>>> whom it is addressed. If you believe this e-mail was sent to you >>>> in error and the e-mail contains patient information, please >>>> contact the Mass General Brigham Compliance HelpLine at >>>> https://www.massgeneralbrigham.org/complianceline >>>> <https://secure-web.cisco.com/1jYq_7i1WV2KuJNwpF_8LuUmEt1uXm4GShRtNXC1xe4Y_B…> >>>> . >>>> >>> >

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Freesurfer March 2024